Phylogeny of the Bangia flora of New Zealand suggests a southern origin for Porphyra and Bangia (Bangiales, Rhodophyta).

Analysis of nuclear small subunit ribosomal RNA gene (18S rDNA) sequence data from 123 samples of the red algal genus Bangia from mainland New Zealand has revealed diversity exceeding that reported for the genus from any other region in the world. Our study resolves two New Zealand Bangia taxa basal to the order Bangiales, and five clades of Bangia, four of which include New Zealand members. The basal taxa are separated from each other by 139 bp and differ from all other Bangia taxa in the New Zealand region by 103-163 bp over approximately 1750 bp 18S rDNA sequence data. Our results reveal a Bangia flora of previously unsuspected richness, and show that the simple morphology of these organisms obscures significant levels of genetic diversity. The presence of high diversity and retention of basal taxa in New Zealand Bangia raises the prospect that the southern hemisphere, and particularly eastern Gondwana, is not only a centre of diversity, but a centre of origin for the modern Bangiales.

An enhanced linkage map of the sheep genome comprising more than 1000 loci.

A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) > or = 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of > 20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of > 1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community.

Ovine neuronal ceroid lipofuscinosis: a large animal model syntenic with the human neuronal ceroid lipofuscinosis variant CLN6.

The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited degenerative neurological diseases affecting children. A number of non-allelic variants have been identified within the human population and the genes for some of these have recently been identified. The underlying mechanism for the neuropathology remains an enigma; however, pioneering studies with the naturally occurring ovine model (OCL) have led to the proposal that these diseases represent lesions in specific hydrophobic protein degradation pathways. In this study, we show linkage between OCL and microsatellite markers on OAR 7q13-15. Using interspecies chromosome painting we establish that OAR 7q13-15 is syntenic with human chromosome 15q21-23, the region which was recently defined as the location of a newly identified late infantile variant (CLN6). We propose that our ovine model represents a mutation in the gene orthologous to that mutated in the human late infantile variant CLN6. The ovine linkage flock, consisting of 56 families, represents a powerful resource for positional cloning of this NCL gene. The availability of such a large animal model will have important implications for experimentation in downstream corrective therapies.

Linkage mapping in sheep and deer identifies a conserved pecora ruminant linkage group orthologous to two regions of HSA16 and a portion of HSA7Q.

Two orthologous linkage groups have been mapped in sheep and deer. Seven loci have been mapped in deer, and 12 in sheep. The sheep linkage group is assigned to ovine chromosome 24. The linkage groups consist of loci from the short arm of human chromosome 16, spanning the region containing the human Batten disease locus, and from human chromosome 7. One locus from the long arm of human chromosome 16 is also present, demonstrating a previously unknown rearrangement between human and ruminant chromosomes. There is no significant difference in marker order and distances between the two linkage groups, implying that this linkage pattern was present in the genome of the common ancestor of the pecora ruminants.

Phylogenetic relationships among transposon-like elements in human and primate DNA.

A THE-1 sequence in intron 7 of the human dystrophin gene has been found to represent a new subfamily of THE-1 elements. The sequence is closely related to the MstII family of repetitive sequences and is more like single-copy sequences found in the galago genome than any other THE-1 sequence previously reported. This new THE-1 sequence has been compared with two other complete THE-1 sequences and three related long-terminal repeat elements that we have previously found in intron 7 of the dystrophin gene, and with members of the same family from elsewhere in the primate genome. Parsimony and deletion analysis show that the cluster of THE-1 sequences in intron 7 of the dystrophin gene has arisen from at least three individual insertion events, rather than from the insertion and duplication of a single progenitor sequence.

Sequence of a transposon identified as Tn1000 (gamma delta).

We report the complete sequence of a transposon found in a cosmid clone of a human DNA sequence. The transposon is identified as the Escherichia coli transposon Tn1000 (also known as gamma delta) on the basis of the identity of the restriction map of the new sequence with that previously recorded for Tn1000 and homology between parts of the new sequence and that of published fragments of Tn1000 sequence. The transposon, which comprises 5,981 nucleotides including two 35 bp inverted terminal repeat sequences (ITRs), contains three open reading frames. The sequence of the resolvase coding region (tnpR) is identical to that published by others. A second reading frame can be identified as the tnpA gene, coding for the transposase, on the grounds of its strong homology with the corresponding gene from transposon Tn3. The third reading frame has the potential to code for a protein of unknown function containing 698 amino acids.

A cluster of transposon-like repetitive sequences in intron 7 of the human dystrophin gene.

A 32 kilobase-pair fragment of intron 7 of the human dystrophin gene has been sequenced and analysed for the presence of repetitive elements and open reading frames. Two transposon-like human elements (THE-1 sequences), and three intervening, and related, long terminal repeat elements, together with three Alu sequences and a LINE sequence have been identified. These represent an unexpected clustering of highly-repetitive sequences within this single segment of intron DNA. Amplification of a region of chimpanzee genomic DNA by the polymerase chain reaction has provided evidence that at least one of the THE-1 sequences is present in the same position in the chimpanzee genome and the high homology between the human and chimpanzee sequences indicates that this element was fixed within the ancestral genome before the divergence of the two species. The possible role of repetitive, transposon-like sequences in natural mutagenesis of the dystrophin gene is discussed.

GELENT: a sequence gel entry program for keyboard and sonic digitizer input.

A program is described for sequence data entry which allows flexible program control by responding to both the keyboard and a sonic digitizer concurrently. Simplification of the initialization stage of each gel reading has been achieved, in comparison with other programs.